<DIV> </DIV><DIV> </DIV><SPAN>On 09/09/11, <B class=name>Sandeep Somani </B><ssomani@gmail.com> wrote:</SPAN>
<BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:CAFKak1qYYOUAiPX7BNa5JcC9rway-ifO_h+Fva6Q99NDNhQE_w@mail.gmail.com type="cite">Hi Mark
<DIV><br /></DIV><DIV>Thanks for the rtp definitions. I added the rtp defs to aminoacids.rtp and renamed residue and atom names in pdb file. </DIV><DIV><br /></DIV><DIV>But pdb2gmx is still complaining about the terminal groups. It seems to have picked up ACE, but not CT3. </DIV><DIV>pdb2gmx error message and modified pdb file are listed below. Any idea ? Do I need to modify .c.tdb ? If so, do you have that entry as well :) ? </DIV></BLOCKQUOTE>
<DIV> </DIV><DIV>Ah, no. To get rid of the warning, you need to teach GROMACS that CT3 is a protein residue. (It knew about ACE from other force fields.) Copy residuetypes.dat from the share/top directory to your working directory, and add CT3 as Protein at the end.</DIV><DIV> </DIV><DIV>To get rid of the error, you need to tell pdb2gmx not to try to change your termini. Use pdb2gmx -ter, and choose "None" for both N and C termini.</DIV><DIV> </DIV><DIV>Mark </DIV><BLOCKQUOTE style="BORDER-LEFT: #00f 1px solid; PADDING-LEFT: 13px; MARGIN-LEFT: 0px" class=iwcQuote cite=mid:CAFKak1qYYOUAiPX7BNa5JcC9rway-ifO_h+Fva6Q99NDNhQE_w@mail.gmail.com type="cite">
<DIV class="mimepart text html">
<DIV> </DIV><DIV><br /></DIV><DIV>Thanks </DIV><DIV>Sandeep </DIV><DIV><br /></DIV><DIV>=============pdb2gmx error=======================================</DIV><DIV>
<DIV>Back Off! I just backed up topol.top to ./#topol.top.3#</DIV><DIV>Processing chain 1 (32 atoms, 4 residues)</DIV><DIV>There are 3 donors and 3 acceptors</DIV><DIV>There are 4 hydrogen bonds</DIV><DIV>Identified residue ACE1 as a starting terminus.</DIV><DIV>Warning: Residue CT32 in chain has different type (Other) from starting residue ACE1 (Protein).</DIV><DIV>Identified residue ALA2 as a ending terminus.</DIV><DIV>8 out of 8 lines of specbond.dat converted successfully</DIV><DIV>Start terminus ACE-1: NH3+</DIV><DIV>End terminus ALA-2: COO-</DIV><DIV><br /></DIV><DIV>-------------------------------------------------------</DIV><DIV>Program pdb2gmx_d, VERSION 4.5.4</DIV><DIV>Source code file: pdb2top.c, line: 1070</DIV><DIV><br /></DIV><DIV>Fatal error:</DIV><DIV>atom N not found in buiding block 1ACE while combining tdb and rtp</DIV><DIV>For more information and tips for troubleshooting, please check the GROMACS</DIV><DIV>website at <a href="http://www.gromacs.org/Documentation/Errors" target=1 >http://www.gromacs.org/Documentation/Errors</A></DIV><DIV>-------------------------------------------------------</DIV></DIV><DIV>================pdb2gmx error====================================</DIV><DIV><br /></DIV><DIV>================modified pdb=====================================</DIV><DIV>
<DIV>
<DIV>REMARK NONE * </DIV><DIV>REMARK DATE: 8/10/11 5:30:23 CREATED BY USER: ss2029 </DIV><DIV><B>ATOM 1 CT3 ACE 1 -2.160 0.537 0.930 1.00 0.00 DIAL</B></DIV><DIV><B>ATOM 2 HT1 ACE 1 -2.466 0.003 0.005 1.00 0.00 DIAL</B></DIV><DIV><B>ATOM 3 HT2 ACE 1 -2.562 1.572 0.910 1.00 0.00 DIAL</B></DIV><DIV><B>ATOM 4 HT3 ACE 1 -2.562 0.001 1.816 1.00 0.00 DIAL</B></DIV><DIV><B>ATOM 5 C ACE 1 -0.672 0.582 1.009 1.00 0.00 DIAL</B></DIV><DIV><B>ATOM 6 O ACE 1 -0.105 1.128 1.954 1.00 0.00 DIAL</B></DIV><DIV>ATOM 7 N ALA 1 0.000 0.000 0.000 1.00 0.00 DIAL</DIV><DIV>ATOM 8 HN ALA 1 -0.453 -0.444 -0.769 1.00 0.00 DIAL</DIV><DIV>ATOM 9 CA ALA 1 1.459 0.000 0.000 1.00 0.00 DIAL</DIV><DIV>ATOM 10 HA ALA 1 1.812 -0.497 0.897 1.00 0.00 DIAL</DIV><DIV>ATOM 11 CB ALA 1 1.949 -0.834 -1.207 1.00 0.00 DIAL</DIV><DIV>ATOM 12 HB1 ALA 1 1.514 -1.854 -1.155 1.00 0.00 DIAL</DIV><DIV>ATOM 13 HB2 ALA 1 1.628 -0.373 -2.167 1.00 0.00 DIAL</DIV><DIV>ATOM 14 HB3 ALA 1 3.056 -0.932 -1.214 1.00 0.00 DIAL</DIV><DIV>ATOM 15 C ALA 1 2.096 1.401 0.000 1.00 0.00 DIAL</DIV><DIV>ATOM 16 O ALA 1 1.425 2.432 0.000 1.00 0.00 DIAL</DIV><DIV>ATOM 17 N ALA 2 3.451 1.458 0.000 1.00 0.00 DIAL</DIV><DIV>ATOM 18 HN ALA 2 3.954 0.594 0.000 1.00 0.00 DIAL</DIV><DIV>ATOM 19 CA ALA 2 4.276 2.664 0.000 1.00 0.00 DIAL</DIV><DIV>ATOM 20 HA ALA 2 4.065 3.236 -0.897 1.00 0.00 DIAL</DIV><DIV>ATOM 21 CB ALA 2 3.864 3.539 1.207 1.00 0.00 DIAL</DIV><DIV>ATOM 22 HB1 ALA 2 2.776 3.756 1.155 1.00 0.00 DIAL</DIV><DIV>ATOM 23 HB2 ALA 2 4.063 3.014 2.167 1.00 0.00 DIAL</DIV><DIV>ATOM 24 HB3 ALA 2 4.407 4.508 1.214 1.00 0.00 DIAL</DIV><DIV>ATOM 25 C ALA 2 5.791 2.399 0.000 1.00 0.00 DIAL</DIV><DIV>ATOM 26 O ALA 2 6.597 3.328 0.000 1.00 0.00 DIAL</DIV><DIV><B>ATOM 27 N CT3 2 6.175 1.110 0.000 1.00 0.00 DIAL</B></DIV><DIV><B>ATOM 28 HN CT3 2 5.528 0.351 0.000 1.00 0.00 DIAL</B></DIV><DIV><B>ATOM 29 CT CT3 2 7.566 0.777 0.000 1.00 0.00 DIAL</B></DIV><DIV><B>ATOM 30 HT1 CT3 2 8.048 1.201 0.907 1.00 0.00 DIAL</B></DIV></DIV><DIV>
<DIV><B>ATOM 31 HT2 CT3 2 7.683 -0.327 0.000 1.00 0.00 DIAL</B></DIV><DIV><B>ATOM 32 HT3 CT3 2 8.048 1.201 -0.907 1.00 0.00 DIAL</B></DIV><DIV>TER 33 CT3 2</DIV><DIV>END</DIV></DIV><DIV>================modified pdb=====================================</DIV></DIV><DIV><br /></DIV><DIV><br /></DIV><DIV><br /><br />
<DIV class=gmail_quote>On Fri, Sep 9, 2011 at 2:52 AM, Mark Abraham <SPAN dir=ltr><<a href="mailto:Mark.Abraham@anu.edu.au" >Mark.Abraham@anu.edu.au</A>></SPAN> wrote:<br />
<BLOCKQUOTE style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class=gmail_quote>
<DIV class=im>On 9/09/2011 8:05 AM, Sandeep Somani wrote:<br />
<BLOCKQUOTE style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class=gmail_quote>Hi<br /><br />I am trying to set up a simulation for dialanine using charmm27 ff but am getting errors in pdb2gmx due to missing definitions in rtp file.<br /><br />I created the pdb file (below) using Charmm for the sequence ACE-ALA-ALA-CT3.<br /><br />pdb2gmx recognizes ALA atoms but not those of the terminal groups ACE and CT3.<br /></BLOCKQUOTE><br /></DIV>Yes, CHARMM in GROMACS has lacked these for some time. I asked over a year ago for them to be added, but that hasn't happened. You can add<br /><br />[ ACE ]<br /> [ atoms ]<br /> CT3 CT3 -0.270 0<br /> HT1 HA 0.090 1<br /> HT2 HA 0.090 2<br /> HT3 HA 0.090 3<br /> C C 0.510 4<br /> O O -0.510 5<br /> [ bonds ]<br /> C CT3<br /> C +N<br /> CT3 HT31<br /> CT3 HT32<br /> CT3 HT33<br /> O C<br /> [ impropers ]<br /> C CT3 +N O<br /><br />[ CT3 ]<br />; this can also be done with the .c.tdb, but the atom naming is different<br />; and this can matter<br /> [ atoms ]<br /> N NH1 -0.470 0<br /> HN H 0.310 1<br /> CT CT3 -0.110 2<br /> HT1 HA 0.090 3<br /> HT2 HA 0.090 4<br /> HT3 HA 0.090 5<br /> [ bonds ]<br /> -C N<br /> N HN<br /> N CAT<br /> CT HT1<br /> CT HT2<br /> CT HT3<br /><br /> [ impropers ]<br /> N -C CAT HN<br /> -C CAT N -O<br /><br />to the end of aminoacids.rtp in a local copy of the charmm27.ff folder to make this work.
<DIV class=im><br /><br />
<BLOCKQUOTE style="BORDER-LEFT: #ccc 1px solid; MARGIN: 0px 0px 0px 0.8ex; PADDING-LEFT: 1ex" class=gmail_quote><br />Does someone have the appropriate definitions for these residues ?<br />( I have tried <a href="http://swissparam.ch/" target=1 >http://swissparam.ch/</A> to generate an itp file for the molecule, but upon using it in GMX it does not give the same energy as that from charmm. )<br /></BLOCKQUOTE><br /></DIV>That will likely be a separate issue.<br /><br />Mark<br /><FONT color=#888888>-- <br />gmx-users mailing list <a href="mailto:gmx-users@gromacs.org" target=1 >gmx-users@gromacs.org</A><br /><a href="http://lists.gromacs.org/mailman/listinfo/gmx-users" target=1 >http://lists.gromacs.org/<U></U>mailman/listinfo/gmx-users</A><br />Please search the archive at <a href="http://www.gromacs.org/Support/Mailing_Lists/Search" target=1 >http://www.gromacs.org/<U></U>Support/Mailing_Lists/Search</A> before posting!<br />Please don't post (un)subscribe requests to the list. Use the www interface or send it to <a href="mailto:gmx-users-request@gromacs.org" target=1 >gmx-users-request@gromacs.org</A>.<br />Can't post? Read <a href="http://www.gromacs.org/Support/Mailing_Lists" target=1 >http://www.gromacs.org/<U></U>Support/Mailing_Lists</A><br /></FONT></BLOCKQUOTE></DIV><br /></DIV></DIV></BLOCKQUOTE>
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